The European Nucleotide Archive

By Rasko Leinonen, Ruth Akhtar, Ewan Birney, Lawrence Bower, A. Cerdeño-Tárraga, Ying Cheng, I. Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson and 11 more. 2010

776 citations recorded by the source corpus.

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe’s primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimental research platform by providing data submission, archive, search and download services. In this article, we outline these services and describe major changes and improvements introduced during 2010. These include extended EMBL-Bank and SRA-data submission services, extended ENA Browser functionality, support for submitting data to the European Genome-phenome Archive (EGA) through SRA, and the launch of a new sequence similarity search service.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “…Kanehisa and Goto, 2000; The Gene Ontology Consortium, 2019) , accessions for cross-referencing entries with external databases (GenBank, ENA, and BioCyc) (Clark et al., 2016; Karp et al., 2019; Leinonen et al., 2011) , name of the gene that encodes for the protein, and proteome accession.”
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, neutral): “Since the submission of metadata with a genome is almost entirely voluntary, and many researches have been electing to submit their genomes to SRA (5) or the European Nucleotide Archive (ENA) (42) instead of assembling and annotating them, we have been searching the literature for publications with ”
The real cost of sequencing: scaling computation to keep pace with data generation (2016, methodology): “This necessitated changes in the storage infrastructure; databases such as the European Nucleotide Archive [9] and the Sequence Read Archive (SRA) [10] were created to store and”
Ensembl regulation resources (2016, background): “Clicking on a peak displays its type (e.g. DNase1 or the specific TF name); the parameters that defined the region from the data including score and peak summit representing the position of highest sequencing read coverage; and a data source such as an ENA accession.”
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata (2011, background): “For all of these projects, the genome sequence is ‘completed’ by depositing the ﬁnal version of the project in one of the public archival databases such as GenBank (17), European Molecular Biology Laboratory (EMBL) (18) and DNA Data Bank of Japan (DDBJ) (19).”
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification (2014, methodology): “As these data are submitted to various public resources like GenBank (7) and EMBL (8) or analysis platforms like Integrated Microbial Genomes (IMG) (9) and MG-RAST (10), it becomes increasingly important to document the associated metadata in order to facilitate comparative analysis and hypothesis g”
Deep Learning in Mining Biological Data (2020, methodology): “The International Nucleotide Sequence Database Collaboration [97], popularly known as INSDC, corroborates biological data from three major sources: i) DNA Databank of Japan [98], ii) European Nucleotide Archive [99], and iii) GenBank [100].”
Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing (2013, neutral): “uk/ena/data/search?query = plasmodium) [33].”
GenBank (2012, methodology): “Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage.”
Cistrome: an integrative platform for transcriptional regulation studies (2011, neutral): “Currently, databases such as the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [33] and the European Bioinformatics Institute (EBI) ArrayExpress [34] host array data, and databases such as the NCBI Sequence Reads Archive (SRA) [35] and the EBI SRA host sequencing”